User: F. Golestan

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F. Golestan10
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Posts by F. Golestan

<prev • 36 results • page 1 of 4 • next >
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Comment: C: Fast download of FASTQ files from the European Nucleotide Archive (ENA)
... Many thanks for your support. ...
written 6 hours ago by F. Golestan10
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Comment: C: Fast download of FASTQ files from the European Nucleotide Archive (ENA)
... Thank you so much for your great help. I removed ascp from export command as you suggested. I also used -i /home/fsgh1d18/.aspera/connect/etc/asperaweb_id_dsa.openssh" " " $1 " ."}' > download.txt in awk command. Now it is perfectly working. Many thanks. ...
written 4 days ago by F. Golestan10
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Comment: C: Fast download of FASTQ files from the European Nucleotide Archive (ENA)
... I also wanted to add that I am using my university cluster which has a linux system. Many thanks. ...
written 5 days ago by F. Golestan10
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Comment: C: Build a Kallisto transcriptome index
... Thanks a lot Friederike for your guide. After downloading transcriptome fasta files, then, the name of fasta file would be for fa.gz file? what about name.idx? Many thanks. ...
written 5 days ago by F. Golestan10
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Comment: C: Build a Kallisto transcriptome index
... Thank you very much Lior. In fact, I want to build an index from both the human and the Cassava Brown Steak Virus separately. I have two different RNA-seq datasets (one for human and another one for Cassava Brown Steak Virus). I need to know how can I obtain transcriptomes for human and the Cassava ...
written 5 days ago by F. Golestan10
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Comment: C: Fast download of FASTQ files from the European Nucleotide Archive (ENA)
... Thanks for your guide. I did as below, But, again -bash: ascp: command not found: $ tar zxvf /scratch/user/ye/ibm-aspera-connect-3.9.5.172984-linux-g2.12-64.tar.gz $ export PATH="/home/user/.aspera/connect/bin/ascp":$PATH $ chmod +x /scratch/user/ye/ibm-aspera-connect-3.9.5.17 ...
written 5 days ago by F. Golestan10 • updated 5 days ago by finswimmer11k
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Build a Kallisto transcriptome index
... Hello, I need to pseudo-align my paired reads to the transcriptome using Kallisto. I know that Kallisto does not use a reference genome sequence, and instead it performs pseudo-alignment to determine the compatibility of reads with targets (e.g. transcript sequences). However, to determine the ...
pseudo-alignment kallisto rna-seq written 5 days ago by F. Golestan10 • updated 5 days ago by Lior Pachter300
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Comment: C: Running Trimmomatic for bulk RNAseq data
... Many thanks to genomax for the helpful guide. I could successfully run trimmomatic for all of my samples. Thanks again. ...
written 7 days ago by F. Golestan10
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Comment: C: Running Trimmomatic for bulk RNAseq data
... Thanks a lot for your great help. The size of my standard error output (stderr) from my job submission is zero. So, It did not produce any error. But. it just successfully performed trimmomatic for one pair of my fq.gz files, and there is no output for another pair (I mean, in the output file, ther ...
written 10 days ago by F. Golestan10
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Comment: C: Running Trimmomatic for bulk RNAseq data
... Thank you for your advise. I ran without -phred64. It could finish the analysis only for one pair of my *18-sortmerna_1.fq.gz and *18-sortmerna_2.fq.gz files. While another pair remains without trimmomatic. I then ran fastqc to check trimmomatic output. It looks good in "per base sequence quality ...
written 10 days ago by F. Golestan10

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